rs7234029

Meta-analysis of 17 studies examining associations between three PTPN2 polymorphisms (rs2542151, rs1893217, rs7234029) and susceptibility to ulcerative colitis and Crohn's disease, involving 18,308 cases and 20,406 controls. The rs2542151 G allele was associated with increased CD risk (OR=1.22, 95% CI 1.15-1.30) and UC risk (OR=1.16, 95% CI 1.07-1.25), with stronger associations in Caucasians than Asians. The rs1893217 C allele showed association with CD (OR=1.45, 95% CI 1.23-1.70), particularly in children (OR=1.56, 95% CI 1.28-1.89), and rs7234029 G allele was associated with CD (OR=1.36, 95% CI 1.16-1.59).

This case-control association study of juvenile idiopathic arthritis (JIA) in 809 JIA cases and 3,521 controls identified susceptibility loci shared with other autoimmune diseases. Three novel loci were identified: PTPN2 (strongest signals rs7234029, p=7.19×10⁻¹¹, OR=1.59; rs1893217, p=3.48×10⁻⁸, OR=1.52; rs2542151, p=3.05×10⁻⁷, OR=1.45), COG6 (rs7993214, p=3.98×10⁻³, OR=0.79), and ANGPT1 (rs1010824, p=4.93×10⁻³, OR=0.77). Four previously reported JIA loci were confirmed: PTPN22, STAT4, C12orf30, and IL2-IL21. Odds ratios ranged from 1.20 to 1.65 in meta-analysis of initial and independent replication cohorts (n=1,015 cases and 1,568 controls).